Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE N-TERMINAL RECA-LIKE DOMAIN OF DJVLGB, A PRANARIAN VASA-LIKE RNA HELICASE
 
Authors :  K. Kurimoto, Y. Muto, N. Obayashi, T. Terada, M. Shirouzu, T. Yabuki, M. E. Seki, T. Matsuda, T. Kigawa, H. Okumura, A. Tanaka, N. Shibata, M. Ka K. Agata, S. Yokoyama, Riken Structural Genomics/Proteomics Ini (Rsgi)
Date :  14 Oct 04  (Deposition) - 12 Apr 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A (1x),B (1x)
Keywords :  Rna Helicase, Dead Box, Vasa, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Kurimoto, Y. Muto, N. Obayashi, T. Terada, M. Shirouzu, T. Yabuki, M. Aoki, E. Seki, T. Matsuda, T. Kigawa, H. Okumura, A. Tanaka, N. Shibata, M. Kashikawa, K. Agata, S. Yokoyama
Crystal Structure Of The N-Terminal Reca-Like Domain Of A Dead-Box Rna Helicase, The Dugesia Japonica Vasa-Like Gene Protein
J. Struct. Biol. V. 150 58 2005
PubMed-ID: 15797730  |  Reference-DOI: 10.1016/J.JSB.2005.01.006

(-) Compounds

Molecule 1 - DJVLGB
    Chains: A, B
    Engineered: YES
    Fragment: N-TERMINAL RECA-LIKE DOMAIN
    Organism Scientific: DUGESIA JAPONICA
    Organism Taxid: 6161
    Other Details: E.COLI CELL FREE SYSTEM

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:230 , GLY A:231 , SER A:232 , GLY A:233 , LYS A:234 , THR A:235 , HOH A:1061 , HOH A:1064 , HOH A:1102 , GLY B:231BINDING SITE FOR RESIDUE SO4 A 1001
2AC2SOFTWARETHR B:230 , GLY B:231 , SER B:232 , GLY B:233 , LYS B:234 , THR B:235BINDING SITE FOR RESIDUE SO4 B 1002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WRB)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1WRB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WRB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1WRB)

(-) Exons   (0, 0)

(no "Exon" information available for 1WRB)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:232
 aligned with O97032_DUGJA | O97032 from UniProtKB/TrEMBL  Length:781

    Alignment length:238
                                   173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393        
         O97032_DUGJA   164 KYDSIPVSVTGPDYSATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVG 401
               SCOP domains d1wrba1 A:164-401 putative ATP-dependent RNA helicase VlgB                                                                                                                                                                                     SCOP domains
               CATH domains 1wrbA00 A:164-401 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........ee............hhhhh.................hhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhh...------......eeee..hhhhhhhhhhhhhhhhh.....eeee.....hhhhhhhhh....eeeehhhhhhhhhhh.........eeeeehhhhhhhh.hhhhhhhhhhh....hhhhheeeeee...hhhhhhhhhhhh...eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wrb A 164 KYDSIPVSVTGPDYSATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDL------KTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVG 401
                                   173       183       193       203       213       223       233       243       | -    |  263       273       283       293       303       313       323       333       343       353       363       373       383       393        
                                                                                                                 251    258                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:232
 aligned with O97032_DUGJA | O97032 from UniProtKB/TrEMBL  Length:781

    Alignment length:236
                                   176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396      
         O97032_DUGJA   167 SIPVSVTGPDYSATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVGR 402
               SCOP domains d1wrbb_ B: automated matches                                                                                                                                                                                                                 SCOP domains
               CATH domains 1wrbB00 B:167-402 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                       CATH domains
           Pfam domains (1) -----------------------------------------DEAD-1wrbB01 B:208-387                                                                                                                                                              --------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------DEAD-1wrbB02 B:208-387                                                                                                                                                              --------------- Pfam domains (2)
         Sec.struct. author .....ee............hhhhh......hhhhhh.....hhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhh..----........eeee..hhhhhhhhhhhhhhhh......eeee.......hhhhhh.....eeeehhhhhhhhhhh.........eeeeehhhhhhhh.hhhhhhhhhhhh........eeeee....hhhhhhhhhhhh...eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wrb B 167 SIPVSVTGPDYSATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDL----YSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVGR 402
                                   176       186       196       206       216       226       236       246    |  256       266       276       286       296       306       316       326       336       346       356       366       376       386       396      
                                                                                                              251  256
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: P-loop_NTPase (1112)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (O97032_DUGJA | O97032)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1wrb)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1wrb
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  O97032_DUGJA | O97032
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  O97032_DUGJA | O97032
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

(no "Entries Sharing at Least One Protein Chain" available for 1WRB)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1WRB)